The relationship between students’ school environment and exercise habits is complex, and is affected by numerous factors. However, the few studies that have been conducted on this relationship have reported inconsistent results, especially regarding Taiwanese students. We conducted this cross-sectional study to investigate the association of school environment and after-school physical activity with health-related physical fitness in Taiwanese adolescents. Data were drawn from a national survey conducted by the Ministry of Education in Taiwan in 2008 of health-related physical fitness measurements among junior high school students (649,442 total) in grades seven to nine. School environment (level of urbanization, school size, presence of sports field or gymnasium) and after-school physical activity were assessed for their association with adolescents’ physical fitness measurements (body mass index (BMI), bent-leg sit-ups, 800-/1600-m run, sit-and-reach, standing long jump). Urban boys and girls perform significantly better in muscle strength and endurance, cardiorespiratory endurance, flexibility, and explosive power; girls from rural areas exhibited significantly worse scores in body composition. Boys from large-size schools performed the worst in cardiorespiratory endurance, flexibility, and explosive power; whereas girls from large-size schools performed the worst in muscle strength, muscle endurance, and explosive power, but had the best score for body composition. However, the differences in body composition of boys from large-, medium-, and small- size schools did not reach a statistically significant level. Adolescents of both genders in schools with a sports field or gymnasium exhibited significantly better in muscle strength and endurance, cardiorespiratory endurance, and explosive power. Boys in schools with a sports field or gymnasium had significantly better body composition; girls in schools with sports field or gymnasium differed significantly in flexibility. Adolescents of both genders who participated in physical activity after school had significantly better body composition, cardiorespiratory endurance, and flexibility. Boys who participated in physical activity after school significantly differed in explosive power, whereas girls who participated in physical activity after school exhibited significantly better flexibility. Thus, the current study demonstrated that some factors, including urbanization (school location in rural or urban areas), school size, school facility provision (school with or without sports fields or gymnasiums), and after-school physical activity participation are more important than others in shaping adolescents’ physical fitness in Taiwan; meanwhile, these association patterns differed by gender.
